PROJECT 1: The Inflammatory Bowel Diseases (IBD), Crohn's disease and ulcerative colitis are genetically complex diseases in which the environment is also a significant contributor. More than 200 genetic variants have been associated with the development of IBD and there have also been considerable insights of microbiome associations with IBD. To date, most genetic studies have used platforms that are designed to capture common genetic signals. We have shown that whole exome sequencing (WES) can identify rare variants that add further to the understanding of the genetic structure of IBD. Our preliminary data also suggests that the creation of polygenic gene risk scores (GRS) can add a powerful dimension to discovering additional genetic signals and also to elucidating the complex relationship with the microbiome. In this proposal we will be utilizing next generation sequencing approaches, single cell technology, together with novel genetic and systems biology approaches to further understand the underlying causes of IBD. We will generate additional WES data in IBD subjects selected as a consequence of their extreme phenotypes or GRS and enriching populations either genetically or by extreme phenotype will likely enhance variant discovery further. We will identify protective variants in healthy controls genetically `primed' to develop CD and also in UC subjects genetically predisposed to severe disease. Genetic variation in genes of the NFkB pathway are enriched in severe UC and we will extract monocytes from UC subjects with high and low NFkB GRSs and perform RNAseq and single cell sequencing on these subjects to better understand the functional consequences of these genetic variants. We will expand upon our striking observation that GRS has a profound effect on the mucosal metabolome in both controls and IBD cases and we will extend these investigations to try and better understand the ability of the serum metabolome to reflect the mucosal signature. Our preliminary data strongly support the hypothesis that disease and pathway specific GRS will identify molecular extremes/clusters of IBD subjects: facilitating novel variant discovery; elucidating functional effects consequent of IBD-associated variants; and delineating genetic effects on host-microbiomal relationships.